Bone marrow-derived mesenchymal stem cells (BMSCs) can migrate to the injured kidney after acute kidney injury (AKI) with limited efficiency. This study investigated the effect of CXCR4 overexpression on BMSC migration to the AKI kidney and the possible mechanisms. CXCR4 gene-modified BMSCs (CXCR4-BMSCs) and null-BMSCs were prepared and transplanted into the AKI mice. Blood indicators, histology, expression of stromal cell-derived factor 1 (SDF-1), and BMSC migration were investigated. Hypoxia/re-oxygenation-pretreated renal tubular epithelial cells (HR-RTECs) were prepared to generate AKI in vitro. The chemotaxis experiment was performed using the transwell chamber. The phosphorylation of AKT and MAPK in the BMSCs was also investigated. The CXCR4-BMSCs showed a remarkable expression of CXCR4. The SDF-1 expression in the AKI renal tissue was increased. CXCR4-BMSCs transplantation sharply increased the accumulation of BMSCs in the renal tissue, which was consistent with a greater improvement of renal function. The in vitro experiments showed that the migration of BMSCs to the HR-RTEC culturing chamber was CXCR4-dependent, and could be fully inhibited by AMD3100, a CXCR4-specific antagonist. The migration could also be partly blocked by either LY294002 (PI3K inhibitor) or PD98059 (MAPK inhibitor). Phosphorylated Akt and MAPK were increased in the BMSCs co-cultured with HR-RTECs and their expression was the highest in the CXCR4-BMSCs, which could be recovered by AMD3100. Overexpression of CXCR4 gene could enhance BMSC migration to the kidney area after AKI. The SDF-1/CXCR4 axis via its activation of PI3K/AKT and MAPK in BMSCs could be the possible mechanisms underlying this function.